Package: ontoProc
Title: processing of ontologies of anatomy, cell lines, and so on
Authors@R: c(person(given="Vincent", family="Carey", role=c("ctb", "cre"),
	   email = "stvjc@channing.harvard.edu",
           comment = c(ORCID = "0000-0003-4046-0063")),
	     person(given="Sara", family="Stankiewicz", role="ctb",
	     email = "reshs@channing.harvard.edu"), person(given="Victor", family="Tarca", role="ctb", 
		email = "vtarca11@gmail.com", comment = c(ORCID = "0009-0003-1976-0392")))
Description: Support harvesting of diverse bioinformatic ontologies,
        making particular use of the ontologyIndex package on CRAN. We
        provide snapshots of key ontologies for terms about cells, cell
        lines, chemical compounds, and anatomy, to help analyze
        genome-scale experiments, particularly cell x compound screens.
        Another purpose is to strengthen development of compelling use
        cases for richer interfaces to emerging ontologies.
Version: 2.4.0
Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache,
        shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT,
        igraph, AnnotationHub, SummarizedExperiment, reticulate,
        R.utils, httr, basilisk, jsonlite, RBGL, ellmer
Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle,
        SingleCellExperiment, celldex, rmarkdown, AnnotationDbi,
        magick,
Depends: R (>= 4.1), ontologyIndex
License: Artistic-2.0
LazyLoad: yes
biocViews: Infrastructure, GO
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Encoding: UTF-8
Collate: 'CLextend.R' 'CLfeats.R' 'autism_details.R'
        'available_ontos.R' 'basilisk.R' 'bind_formal_tags.R'
        'bioregistry.R' 'clfixer.R' 'common_classes.R'
        'connect_classes.R' 'countClasses.R' 'ctmarks.R' 'data.R'
        'dropStop.R' 'fastGrep.R' 'findCommonAncestors.R' 'formalize.R'
        'getOntos.R' 'get_ordo_owl_path.R' 'graphNEL.R' 'mapNaive.R'
        'nio_details.R' 'ontoDiff.R' 'owl2cache.R' 'owl_ops.R'
        'plot.owlents.R' 'quickOnto.R' 'roots.R' 'setup_entities2.R'
        'seurTab.R' 'shiny.R' 'subset_descendants.R' 'sym2CellOnto.R'
        'termProc.R' 'treeproc.R'
URL: https://github.com/vjcitn/ontoProc
BugReports: https://github.com/vjcitn/ontoProc/issues
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 23:20:08 UTC
RemoteUrl: https://github.com/bioc/ontoProc
RemoteRef: RELEASE_3_22
RemoteSha: f2c1b3f170ce3e23ed97712695fb8309b0888c6d
NeedsCompilation: no
Packaged: 2026-01-24 08:31:42 UTC; root
Author: Vincent Carey [ctb, cre] (ORCID:
    <https://orcid.org/0000-0003-4046-0063>),
  Sara Stankiewicz [ctb],
  Victor Tarca [ctb] (ORCID: <https://orcid.org/0009-0003-1976-0392>)
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>
Built: R 4.5.2; ; 2026-01-24 08:34:43 UTC; windows
